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Meta-MEME is a software toolkit for building and using motif-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences, as well as a set of motif models discovered by MEME. Meta-MEME combines these models into a single, motif-based hidden Markov model and uses this model to search a sequence database for homologs.
To run this software interactively in a Linux environment run the commands:
module load meme mhmme
The following executables are available:
Papers are available at: http://meme.sdsc.edu/meme/mhmm-papers.html